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Table 3 Mutations of OCA2 segregating in Pakistani families

From: Molecular genetic studies and delineation of the oculocutaneous albinism phenotype in the Pakistani population

Nucleotide change# Frequency in control samples Effect on protein Location Family Ethinicity Haplotype* S1-S2-S3-S4-S5-S6-S7-S8 Polyphen 2 SNPs3D Mutation Taster Allele frequency this study Regulatory region sequence¥
Missense
c.954 G > A 0/200 p.Met318Ile loop TM2-3 PKAB063 Warraich C-C-C-G-A-T-G-A Benign Benign Polymorphism 7.14% TAAA TG
c.1456 G > T 0/344 p.Asp486Tyr within TM7 PKAB052 Lanjay T-C-T-A-A-C-A-G Damaging Damaging Pathogenic 35.71% TAAG TG
     PKAB054 Mehay T-C-T-A-A-C-A-G      TAAG TG
     PKAB055 Mehay T-C-T-A-A-C-A-G      TAAG TG
     PKAB067 Ghallu T-C-T-A-A-C-A-G      TAAG TG
     PKAB101 Chaaki T-C-T-A-A-C-A-G      TAAA TG
c.1580 T > G 0/298 p.Leu527Arg within TM8 PKAB063 Warraich C-C-C-G-A-T-G-A     7.14% TAAA TG
c.2228 C > T   p.Pro743Leu loop TM12-13 PKAB058 Arain C-C-T-G-A-C-A-A Damaging Damaging Pathogenic 14.30% TAAA TG
     PKAB072 Joyia C-C-T-G-A-C-A-A      TAAA TG
c.2359 G > A   p.Ala787Thr within TM13 PKAB071 Chohan C-C-C-G-A-C-G-A Damaging Damaging Pathogenic 7.14% TAAA TG
Splice site
c.1045-15 T > G 0/364 splicing within TM3 PKAB060 Bubar C-C-T-G-A-T-G-A Damaging Damaging Pathogenic 35.71% TAAA TG
   error§   PKAB068 Sindhu Jutt C-C-T-G-A-T-G-A      TAAA TG
     PKAB079 Abbasi C-C-T-G-A-T-G-A      TAAA TG
     PKAB151 Ansari T-C-T-G-A-T-G-A      TAAA TG
     PKAB152 Ansari C-C-T-G-A-T-G-A      TAAA TG
  1. #Given in bold are the novel variants found in this study. *SNPs used for haplotyping: S1, rs17565841; S2, rs12592307 (p.S788S); S3, rs1800411 (p.C517C); S4, rs1900758; S5, rs1800410; S6, rs10852218; S7, rs1800404; S8, rs12913832. According to Feb. 2009 UCSC Human Genome browser assembly (GRCh37/hg19), the S2 to S6 are present within the coding (S2 and S3) or intronic regions of OCA2. §Human Splicing Finder program (http://www.umd.be/HSF/) predicted a cryptic splice donor site 12 nucleotide upstream of known splice acceptor site for exon 9 due to the mutation. ¥Conserved regulatory element sequence present within intron 86 of the HERC2 gene. N/A not applicable. TM transmembrane domain. TMpred-Prediction of transmembrane regions and orientation (http://www.ch.embnet.org/software/TMPRED_form.html) was used for OCA2 domain prediction.